Is EBP p.Arg110Gln (c.329G>A) pathogenic?

EBP p.Arg110Gln (c.329G>A) is classified Pathogenic/Likely pathogenic in EBP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-06-18). AlphaMissense: likely pathogenic (0.7582); Absent from gnomAD v4.1; Associated with X-linked chondrodysplasia punctata 2.

What condition is associated with EBP p.Arg110Gln (c.329G>A)?

EBP p.Arg110Gln (c.329G>A) is associated with X-linked chondrodysplasia punctata 2 (ClinVar).

How common is EBP p.Arg110Gln (c.329G>A) in the general population?

EBP p.Arg110Gln (c.329G>A) is absent from gnomAD v4.1 (gnomAD).

How is X-linked dominant chondrodysplasia punctata inherited?

Typically X-linked dominant (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about EBP p.Arg110Gln (c.329G>A)?

AlphaMissense predicts likely pathogenic (score 0.7582) — an in-silico prediction, not a clinical call.

EBP p.Arg110Gln

c.329G>A · rs1602090481 · VCV807598

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.7582 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

X-linked chondrodysplasia punctata 2

Computational evidence

Protein change
AlphaMissense	0.7582	likely pathogenic ✓ concordant with ClinVar · top 9% in EBP
REVEL	0.972	strongly pathogenic-leaning
SaProt	LLR -12.66	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP 2.1, phastCons 1
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EBP
Protein: p.Arg110Gln
Coding: c.329G>A
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs1602090481
Type: single nucleotide variant
Location: chrX:48527016 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 110: the 'disordered' region

Full EBP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

X-linked chondrodysplasia punctata 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked dominant chondrodysplasia punctata (Orphanet):

Inheritance: X-linked dominant
Onset: Antenatal, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

EBP p.Arg110Ter Pathogenic ★★ same residue
EBP p.Arg147His Pathogenic ★★ ⚠ same condition
EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same condition
EBP p.Gly161Arg Likely pathogenic ★★ same condition
EBP p.Trp186Ter Pathogenic ★★ same condition
EBP p.Trp61Ter Pathogenic/Likely pathogenic ★★ same condition
EBP p.Trp68Cys Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ebp-p-arg110gln (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown